path_proj = here::here()
path_source = file.path(path_proj, "source")

# source
source(file.path(path_source, "simulation", "simulations_functions_final.R"))
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
## 
## Attaching package: 'tidyr'
## The following object is masked from 'package:reshape2':
## 
##     smiths
## The following object is masked from 'package:rstan':
## 
##     extract
# source from other paper
source(file.path(path_source, "funcs_german_paper", "plotReportingTriangle.R"))
# setting: delay,  number of days
seed <- 4
D <- 15
N_obs <- 200

# generate alpha
alpha_lambda <- generate_alpha(N_obs, range = c(40, 200), dist = "uniform", seed = seed)
plot(density(alpha_lambda))

# time varying b
beta0 = -2 ; beta1 = 0.01
data <- simsDataGenQ( alpha = alpha_lambda,
                     #alpha =  c(1:10, seq(1, 232, by = 4)),
                      days = N_obs, method = "random_walk",
                     b = 0.1, sigma_rw = 0.1, seed = seed)
# create triangular data
data_trunc <- create_triangular_data(data$case_reported)

# get indices of non-NAs 
indices_data_trunc <- find_non_na_coords(data_trunc)

data_trunc[is.na(data_trunc)] <- 0

basis for spline

# setting
time_points <- 1:N_obs
n_knots <- 5

# create basis
X_spline <- create_basis(N_obs, n_knots)

basis_df <- data.frame(time = time_points, X_spline)
basis_long <- reshape2::melt(basis_df, id.vars = "time")

# draw basis
ggplot(basis_long, aes(x = time, y = value, color = variable)) +
  geom_line() +
  labs(title = "B-spline Basis Functions for Time",
       x = "Time (Days)",
       y = "Basis Value") +
  theme_minimal()

source(file.path(path_source, "functions", "plot_function.R"))
source(file.path(path_source, "functions", "moving_window_function.R"))
# imagine 60 days since 2024-01-01

# now <- as.Date("2024-02-01")
scoreRange <- seq(as.Date("2024-01-20"),as.Date("2024-02-28"),by="1 day")

path_p_change <- file.path(path_proj, "source", "models",
                     "trunc", "stan_model_dep-spline-trunc-modi.stan")

path_p_fixed <- file.path(path_proj, "source", "models", "trunc",
                     "stan_model_time-ind-p-trunc.stan")

dates <- as.Date(rownames(data$case_reported))
selected_dates <- dates[c(150,175,200)]  # pick certain days

out <- nowcasting_moving_window(data$case_reported, scoreRange = selected_dates, 
                                case_true = data$case_true,
                         N_obs = N_obs, D = 15, sigma_b = 0.1, seeds = 123,
                         iter= 2000, warmup = 1000, refresh = 0,
                         path_p_change = path_p_change, path_p_fixed = path_p_fixed)
## ====================
## now=2024-05-29 (1/3)
## ====================
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## Warning: There were 2991 divergent transitions after warmup. See
## https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
## to find out why this is a problem and how to eliminate them.
## Warning: There were 9 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
## https://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
## Warning: Examine the pairs() plot to diagnose sampling problems
## Warning: The largest R-hat is 3.1, indicating chains have not mixed.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#r-hat
## Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#bulk-ess
## Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#tail-ess
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
## ℹ Please use the `linewidth` argument instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
## Warning: A numeric `legend.position` argument in `theme()` was deprecated in ggplot2
## 3.5.0.
## ℹ Please use the `legend.position.inside` argument of `theme()` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
## ====================
## now=2024-06-23 (2/3)
## ====================
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## Warning: There were 3000 divergent transitions after warmup. See
## https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
## to find out why this is a problem and how to eliminate them.
## Warning: Examine the pairs() plot to diagnose sampling problems
## Warning: The largest R-hat is 3.27, indicating chains have not mixed.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#r-hat
## Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#bulk-ess
## Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#tail-ess
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## ====================
## now=2024-07-18 (3/3)
## ====================
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## Warning: There were 2021 divergent transitions after warmup. See
## https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
## to find out why this is a problem and how to eliminate them.
## Warning: There were 979 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
## https://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
## Warning: Examine the pairs() plot to diagnose sampling problems
## Warning: The largest R-hat is 3.35, indicating chains have not mixed.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#r-hat
## Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#bulk-ess
## Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#tail-ess
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
data <- data$case_reported
out$plots
## [[1]]

## 
## [[2]]

## 
## [[3]]

# real data
real_data_path <- normalizePath(file.path(path_source, "..", "data", "raw")) # data path

load(file.path(real_data_path,"husO104Hosp.Rdata"))
husO104_triangular <- listToTriangle(husO104Hosp)
husO104_tri_cumu <- cumulative_matrix(husO104_triangular)

selected_dates <- seq(as.Date("2011-05-20"),as.Date("2011-06-30"),by="5 day")

out <- nowcasting_moving_window(husO104_tri_cumu, scoreRange = selected_dates, 
                                case_true = as.vector(husO104_tri_cumu[,ncol(husO104_tri_cumu)]),
                         N_obs = nrow(husO104_tri_cumu), D = 15, sigma_b = 0.1, seeds = 123,
                         iter= 3000, warmup = 1500, num_chains = 3, refresh = 0,
                         path_p_change = path_p_change, path_p_fixed = path_p_fixed)
## ====================
## now=2011-05-20 (1/9)
## ====================
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## Warning: There were 4493 divergent transitions after warmup. See
## https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
## to find out why this is a problem and how to eliminate them.
## Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See
## https://mc-stan.org/misc/warnings.html#bfmi-low
## Warning: Examine the pairs() plot to diagnose sampling problems
## Warning: The largest R-hat is 1.83, indicating chains have not mixed.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#r-hat
## Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#bulk-ess
## Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#tail-ess
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## ====================
## now=2011-05-25 (2/9)
## ====================
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## Warning: There were 4499 divergent transitions after warmup. See
## https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
## to find out why this is a problem and how to eliminate them.
## Warning: Examine the pairs() plot to diagnose sampling problems
## Warning: The largest R-hat is 2.38, indicating chains have not mixed.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#r-hat
## Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#bulk-ess
## Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#tail-ess
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## ====================
## now=2011-05-30 (3/9)
## ====================
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## Warning: There were 4500 divergent transitions after warmup. See
## https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
## to find out why this is a problem and how to eliminate them.
## Warning: Examine the pairs() plot to diagnose sampling problems
## Warning: The largest R-hat is 2.36, indicating chains have not mixed.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#r-hat
## Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#bulk-ess
## Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#tail-ess
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## ====================
## now=2011-06-04 (4/9)
## ====================
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## Warning: There were 4445 divergent transitions after warmup. See
## https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
## to find out why this is a problem and how to eliminate them.
## Warning: There were 55 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
## https://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
## Warning: Examine the pairs() plot to diagnose sampling problems
## Warning: The largest R-hat is 2.75, indicating chains have not mixed.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#r-hat
## Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#bulk-ess
## Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#tail-ess
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## ====================
## now=2011-06-09 (5/9)
## ====================
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## Warning: There were 4500 divergent transitions after warmup. See
## https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
## to find out why this is a problem and how to eliminate them.
## Warning: Examine the pairs() plot to diagnose sampling problems
## Warning: The largest R-hat is 2.75, indicating chains have not mixed.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#r-hat
## Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#bulk-ess
## Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#tail-ess
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## ====================
## now=2011-06-14 (6/9)
## ====================
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## Warning: There were 4500 divergent transitions after warmup. See
## https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
## to find out why this is a problem and how to eliminate them.
## Warning: Examine the pairs() plot to diagnose sampling problems
## Warning: The largest R-hat is 2.82, indicating chains have not mixed.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#r-hat
## Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#bulk-ess
## Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#tail-ess
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## ====================
## now=2011-06-19 (7/9)
## ====================
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## Warning: There were 4500 divergent transitions after warmup. See
## https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
## to find out why this is a problem and how to eliminate them.
## Warning: Examine the pairs() plot to diagnose sampling problems
## Warning: The largest R-hat is 3.5, indicating chains have not mixed.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#r-hat
## Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#bulk-ess
## Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#tail-ess
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## ====================
## now=2011-06-24 (8/9)
## ====================
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## Warning: There were 4500 divergent transitions after warmup. See
## https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
## to find out why this is a problem and how to eliminate them.
## Warning: Examine the pairs() plot to diagnose sampling problems
## Warning: The largest R-hat is 3.35, indicating chains have not mixed.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#r-hat
## Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#bulk-ess
## Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#tail-ess
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## ====================
## now=2011-06-29 (9/9)
## ====================
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
## Warning: There were 4500 divergent transitions after warmup. See
## https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
## to find out why this is a problem and how to eliminate them.
## Warning: Examine the pairs() plot to diagnose sampling problems
## Warning: The largest R-hat is 2.9, indicating chains have not mixed.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#r-hat
## Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#bulk-ess
## Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
## Running the chains for more iterations may help. See
## https://mc-stan.org/misc/warnings.html#tail-ess
## Trying to compile a simple C file
## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
## using SDK: ‘MacOSX13.3.sdk’
## clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## #include <cmath>
##          ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1
out$plots
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